When Microscopic Colitis Takes Over Your Life: Looking Beyond Chronic Diarrhea and Migraines
Imagine being afraid to leave your house because you don't know when you will need a bathroom.
Imagine being unable to make it through a 30-minute period without experiencing sudden, severe diarrhea.
Imagine becoming so worried about an accident that you stop eating during the day and limit how much water you drink—because eating and drinking seem to make everything worse.
This is what one of my patients with microscopic colitis was experiencing when she came to see me.
Her condition had become about much more than diarrhea. It was affecting her ability to work, travel, socialize, eat, drink, and live normally. She was also dealing with severe migraines that had become increasingly difficult to control.
Her story illustrates why, in some patients with chronic digestive symptoms, it can be important to look beyond simply controlling the diarrhea and ask:
What else could be contributing to the inflammation, altered gut environment, nutrient depletion, and symptoms occurring throughout the body?
Living in Fear of the Next Bathroom Trip
This patient had been diagnosed with microscopic colitis and had been taking a corticosteroid medication daily to help control her diarrhea.
Her gastroenterologist wanted to get her off long-term steroid therapy, which is understandable. However, the prospect of reducing the medication caused enormous anxiety for her because she knew what happened when her symptoms were not controlled.
Without adequate control, she could experience multiple episodes of watery, sometimes explosive diarrhea.
The unpredictability was one of the most debilitating parts.
She couldn't comfortably go somewhere without knowing where the nearest bathroom was. Even a 30-minute period could feel risky.
Over time, she began changing her behavior to try to prevent symptoms.
She stopped eating during the day because food seemed to trigger diarrhea.
She also began limiting fluids because she was afraid that drinking would lead to another urgent bathroom trip.
Unfortunately, this creates another problem.
Avoiding food and water can create its own cycle
Chronic diarrhea can result in substantial losses of water and electrolytes. When someone begins restricting both food and fluids to avoid diarrhea, they can potentially worsen dehydration, inadequate calorie intake, electrolyte imbalance, fatigue, and nutritional deficiencies.
It becomes a vicious cycle:
Diarrhea → fear of symptoms → food and fluid restriction → nutritional and hydration challenges → increased physical stress → greater difficulty recovering.
This was an important part of understanding this patient's overall picture.
Temporary Relief Wasn't Solving the Problem
She had found that occasional Pepto-Bismol could help somewhat.
She had also experienced temporary improvement after courses of antibiotics.
Interestingly, after taking antibiotics for an unrelated issue, her diarrhea improved for approximately two to three weeks—only to return again.
Each time, the symptoms could come back even more intensely.
That pattern raised an important question.
Why would symptoms temporarily improve when the intestinal microbial environment was altered, only to return later?
This did not mean that antibiotics were the long-term answer. In fact, repeated or unnecessary antibiotic exposure can further disrupt the gut microbiome and can increase the risk of complications such as Clostridium difficileinfection.
Instead, the temporary response suggested that the intestinal microbial environment could be one piece of the larger clinical picture.
Microscopic Colitis and the Gut Microbiome
Microscopic colitis is an inflammatory condition of the colon that commonly causes chronic, watery, non-bloody diarrhea. It includes two primary forms: collagenous colitis and lymphocytic colitis.
Unlike some other gastrointestinal conditions, the colon may look relatively normal during a colonoscopy. Diagnosis depends on examining biopsies under a microscope.
Traditional treatment often focuses on reducing intestinal inflammation and controlling diarrhea. Budesonide, a locally acting corticosteroid, is an important evidence-based treatment for microscopic colitis.
However, relapse after stopping treatment is common, particularly in patients with ongoing disease activity. This is one reason some patients can find themselves caught in a cycle of treatment, improvement, medication withdrawal, and recurrence.
Emerging research is also examining the relationship between microscopic colitis and the gut microbiome.
Recent reviews describe differences in microbial composition and diversity in people with microscopic colitis and suggest that changes in the intestinal microbial environment may interact with the immune system and intestinal inflammation.
This does not mean that dysbiosis is the single cause of microscopic colitis.
It does mean that the gut environment may be worth considering as part of the bigger picture.
What We Found When We Looked More Deeply
When we evaluated this patient's gastrointestinal health, we found several additional pieces that were important to consider.
Testing showed:
Evidence of C. difficile
Overgrowth of potentially problematic bacteria
Elevated inflammatory markers
Elevated secretory IgA
Significant nutritional and antioxidant deficiencies
Her nutrient testing also showed low levels of several nutrients involved in antioxidant defense, mitochondrial function, nervous system health, and cellular function, including:
Omega-3 fatty acids
Glutathione
Vitamin C
Alpha-lipoic acid
Several B vitamins
Magnesium
These findings did not mean that every deficiency was responsible for her symptoms.
Instead, they gave us additional information about the physiological stress her body was experiencing.
Chronic diarrhea, restricted food intake, chronic inflammation, and altered digestion can all make maintaining adequate nutritional status more difficult.
And that matters because the gut isn't an isolated system.
The Gut-Brain Connection and Her Severe Migraines
This patient was also experiencing severe migraines.
Historically, Imitrex had worked well for her. However, over the previous year, it had become less effective.
Her migraines were becoming so severe that some could last an entire week.
She also noticed improvement from chiropractic care, which was another important piece of her individualized care.
She had a history of mold exposure as well, adding another environmental factor to consider when looking at her overall health history.
But the connection between her digestive symptoms and migraines was particularly interesting.
The gut and brain constantly communicate
The gut-brain axis describes the two-way communication between the gastrointestinal tract, immune system, nervous system, hormones, and gut microbiome.
And migraine research is increasingly investigating this relationship.
Recent systematic reviews have found differences in the gut microbiome of people with migraine compared with people without migraine. Some studies have found differences in microbial diversity and specific bacterial groups.
Researchers are investigating several possible mechanisms, including:
Intestinal barrier function
Immune activation
Neuroinflammation
Oxidative stress
Microbial metabolites
Neurotransmitter signaling
Communication through the vagus nerve
Interactions between the microbiome and the nervous system
Importantly, research is still evolving. We cannot currently say that gut dysbiosis causes migraine or that treating the microbiome will eliminate migraines.
But the evidence increasingly supports the idea that the gut and brain should not always be considered completely separate systems.
Why Her Nutritional Status Mattered
Another important part of this patient's case was the number of nutrients that were low.
Omega-3 fatty acids, magnesium, B vitamins, vitamin C, glutathione, and alpha-lipoic acid are involved in a variety of physiological processes, including cellular energy production, antioxidant defense, nervous system function, and regulation of inflammation.
Some of these nutrients have also been studied in the context of migraine.
Magnesium, for example, has an established place in migraine research and prevention strategies for some patients. Research has also explored the roles of riboflavin and other mitochondrial or metabolic nutrients in migraine.
That doesn't mean that correcting a nutrient deficiency will automatically resolve a migraine.
But when someone is experiencing:
chronic diarrhea + restricted food intake + inflammation + altered gut function + severe migraines
it makes sense to ask whether nutritional status could be contributing to the overall physiological burden.
The Goal Isn't Simply to Stop the Diarrhea
This is an important distinction in functional medicine.
Stopping diarrhea is obviously important.
But if the only goal is to suppress the symptom, we may miss important factors contributing to the patient's overall health.
In this case, we wanted to understand the bigger picture:
What was happening in the gut?
Was there evidence of infection or microbial imbalance?
What was happening with intestinal inflammation?
Was she absorbing and maintaining adequate nutrients?
How was chronic diarrhea affecting hydration and nutrition?
What other symptoms were occurring at the same time?
Could the gut-brain connection be relevant to her migraines?
And perhaps most importantly:
How could we support her health while she continued working with her gastroenterologist on appropriate management of her microscopic colitis?
A Functional Medicine Approach to Microscopic Colitis
Functional medicine does not mean replacing conventional treatment for microscopic colitis.
For someone with severe microscopic colitis, appropriate gastroenterology care is essential.
Instead, a functional medicine approach can look at the additional factors surrounding the condition.
Depending on the individual, this may include evaluating:
Gut infections
Microbial imbalance
Digestive function
Inflammation
Nutrient status
Hydration and electrolyte status
Dietary adequacy
Medication and supplement history
Environmental exposures
Stress and nervous-system regulation
Migraine triggers
The gut-brain connection
The goal is to develop an individualized plan based on what is actually happening in that person's body—not assume that every person with microscopic colitis has the same underlying contributors.
Her Story Is a Reminder That Chronic Diarrhea Is More Than a Digestive Symptom
For this patient, microscopic colitis wasn't simply a diagnosis on a medical chart.
It was affecting almost every part of her life.
She was afraid to eat.
She was afraid to drink.
She was afraid to leave the house.
She was constantly thinking about where the nearest bathroom was.
And at the same time, she was experiencing severe, prolonged migraines that were becoming increasingly difficult to control.
When chronic gastrointestinal symptoms reach this level, it is worth looking at the entire picture.
The goal isn't to promise a quick fix or suggest that one test or supplement will solve everything.
The goal is to understand the many factors that may be contributing to the patient's symptoms and give the body the nutritional, digestive, and physiological support it needs—while continuing appropriate medical care for the underlying disease.
If You Are Struggling With Microscopic Colitis, Chronic Diarrhea, or Migraines
If you have microscopic colitis and feel like you are stuck between medications, recurring diarrhea, food restriction, and fear of leaving the house, you don't have to ignore the other pieces of your health.
A functional medicine evaluation can help look at the broader picture, including digestive health, gut microbiome factors, inflammation, nutritional status, and the gut-brain connection.
At Alternative Family Medicine, we work with patients in Arvada, Longmont, Boulder, Erie, Fredrick, Firestone Wheat Ridge, Golden, Westminster, and throughout the Denver area who are looking for a more comprehensive approach to chronic digestive symptoms and overall health.
This article is for educational purposes only and is not a substitute for medical care. Microscopic colitis can cause significant fluid and electrolyte losses and should be managed with an appropriately qualified medical professional. Do not stop corticosteroids or other prescribed medications without guidance from your prescribing clinician.